Brain data
Contents
Brain data¶
This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.
Gray matter qMRI¶
Code imports¶
# Python imports
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd
# Import custom tools
from tools.data import Data
from tools.plot import Plot
Download data¶
data_type = 'brain'
release_version = 'latest'
dataset = Data(data_type)
dataset.download(release_version)
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Load data plot it¶
dataset.load()
dataset.data_type
'brain'
fig_gm = Plot(dataset, plot_name = 'new-fig-2')
fig_gm.title = 'Brain gray matter qMRI microstructure'
fig_gm.display('jupyter-book', tissue = 'GM')
White matter qMRI¶
fig_wm = Plot(dataset, plot_name = 'new-fig-4')
fig_wm.title = 'Brain white matter qMRI microstructure'
fig_wm.display('jupyter-book', tissue = 'WM')
Spine¶
data_type = 'spine'
release_version = 'latest'
dataset = Data(data_type)
dataset.download(release_version)
dataset.load()
dataset.data['T1w']
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| Subject | Session | Timestamp | SCT Version | Filename | Slice (I->S) | VertLevel | MEAN(area) | STD(area) | MEAN(angle_AP) | ... | STD(diameter_AP) | MEAN(diameter_RL) | STD(diameter_RL) | MEAN(eccentricity) | STD(eccentricity) | MEAN(orientation) | STD(orientation) | MEAN(solidity) | STD(solidity) | SUM(length) | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1 | 1 | 2021-06-09 23:24:10 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 31:75 | 2:3 | 67.680431 | 1.598728 | -4.254822 | ... | 0.225578 | 10.843164 | 0.307774 | 0.680936 | 0.039585 | 2.149545 | 1.734302 | 0.980308 | 0.009615 | 36.167347 |
| 6 | 1 | 2 | 2021-06-09 23:24:19 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 47:86 | 2:3 | 67.511930 | 1.726861 | -6.577358 | ... | 0.186145 | 10.874612 | 0.275935 | 0.690540 | 0.031751 | 2.855729 | 1.967201 | 0.977647 | 0.008612 | 32.528253 |
| 0 | 1 | 3 | 2021-06-09 23:24:08 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 51:93 | 2:3 | 64.109061 | 3.127582 | -4.670983 | ... | 0.464761 | 10.640776 | 0.333651 | 0.690605 | 0.054994 | 3.202127 | 2.184708 | 0.976971 | 0.007494 | 34.565242 |
| 8 | 2 | 1 | 2021-06-09 23:41:15 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 1:38 | 2:3 | 66.455289 | 4.204379 | 0.095829 | ... | 0.684070 | 11.992443 | 0.585042 | 0.794791 | 0.061804 | 2.234122 | 1.464966 | 0.963074 | 0.016533 | 31.424022 |
| 10 | 2 | 2 | 2021-06-09 23:41:24 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 12:50 | 2:3 | 73.688109 | 2.833139 | -0.068322 | ... | 0.406465 | 12.065046 | 0.492764 | 0.756302 | 0.053939 | 2.367144 | 1.803792 | 0.966030 | 0.009791 | 32.356730 |
| 15 | 2 | 3 | 2021-06-09 23:50:43 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 3:39 | 2:3 | 73.905494 | 2.073274 | -0.691532 | ... | 0.368828 | 12.371408 | 0.639116 | 0.780126 | 0.052688 | 1.694898 | 1.187327 | 0.963111 | 0.014391 | 30.534960 |
| 12 | 2 | 4 | 2021-06-09 23:41:39 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 9:46 | 2:3 | 69.405673 | 4.568637 | -0.749008 | ... | 0.543059 | 12.227376 | 0.665839 | 0.796428 | 0.053488 | 2.145301 | 1.623586 | 0.958420 | 0.020529 | 31.442066 |
| 9 | 3 | 1 | 2021-06-09 23:41:20 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 51:85 | 2:3 | 59.927681 | 1.980624 | -0.778617 | ... | 0.334499 | 10.086060 | 0.232852 | 0.658816 | 0.049798 | 2.475063 | 1.644264 | 0.972640 | 0.009458 | 28.297791 |
| 13 | 3 | 2 | 2021-06-09 23:41:42 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 33:66 | 2:3 | 60.228814 | 1.776652 | -1.464265 | ... | 0.247391 | 10.486967 | 0.214164 | 0.716856 | 0.033921 | 1.850661 | 1.538691 | 0.966100 | 0.007298 | 27.236579 |
| 11 | 3 | 3 | 2021-06-09 23:41:39 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 43:77 | 2:3 | 60.621684 | 1.733616 | -0.009478 | ... | 0.358365 | 10.632869 | 0.308162 | 0.726909 | 0.049649 | 1.681134 | 1.217510 | 0.970807 | 0.010769 | 28.389363 |
| 16 | 3 | 4 | 2021-06-09 23:55:17 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 40:74 | 2:3 | 59.915665 | 2.030933 | -2.222570 | ... | 0.296578 | 10.445562 | 0.243935 | 0.716104 | 0.038919 | 2.551453 | 2.010580 | 0.972863 | 0.010084 | 28.329492 |
| 17 | 4 | 2 | 2021-06-09 23:55:38 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 49:84 | 2:3 | 59.717857 | 2.220913 | 2.572138 | ... | 0.399145 | 10.999128 | 0.354854 | 0.775108 | 0.045832 | 2.195005 | 1.555832 | 0.972639 | 0.015228 | 29.056988 |
| 18 | 4 | 3 | 2021-06-09 23:55:53 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 43:77 | 2:3 | 61.969221 | 2.026699 | 6.989458 | ... | 0.326731 | 10.956739 | 0.419218 | 0.753243 | 0.040568 | 2.095929 | 1.251544 | 0.976777 | 0.009427 | 28.313078 |
| 4 | 5 | 1 | 2021-06-09 23:24:18 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 19:57 | 2:3 | 53.010013 | 11.097434 | -1.790824 | ... | 1.087683 | 10.965275 | 0.675722 | 0.822167 | 0.059414 | 4.036279 | 2.295310 | 0.952220 | 0.027352 | 33.355815 |
| 14 | 5 | 2 | 2021-06-09 23:41:45 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 44:82 | 2:3 | 64.717972 | 4.153035 | -3.034680 | ... | 0.567947 | 11.448594 | 0.408139 | 0.769825 | 0.056204 | 4.103625 | 1.847953 | 0.966696 | 0.012619 | 32.529064 |
| 2 | 6 | 1 | 2021-06-09 23:24:11 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 45:81 | 2:3 | 62.953114 | 1.769023 | -0.646246 | ... | 0.216321 | 11.513113 | 0.470660 | 0.792890 | 0.029588 | 1.260913 | 1.049494 | 0.965233 | 0.014776 | 30.644730 |
| 7 | 6 | 2 | 2021-06-09 23:24:21 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 89:125 | 2:3 | 64.823566 | 18.835219 | 13.113466 | ... | 1.159209 | 9.503113 | 2.506067 | 0.576338 | 0.152557 | 22.042768 | 32.322329 | 0.968538 | 0.032237 | 10.122137 |
| 5 | 6 | 3 | 2021-06-09 23:24:19 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 38:75 | 2:3 | 62.990802 | 2.049191 | -2.338349 | ... | 0.298265 | 11.506661 | 0.596266 | 0.792194 | 0.041279 | 1.614134 | 1.158783 | 0.973527 | 0.010495 | 31.364216 |
| 3 | 6 | 4 | 2021-06-09 23:24:12 | git-jca/3413-run-batch-session-c41958db922273a... | /Users/julien/temp/neuromod/data_processed/sub... | 58:95 | 2:3 | 63.925810 | 2.765595 | -1.132526 | ... | 0.248317 | 11.727604 | 0.490648 | 0.803257 | 0.028672 | 1.754369 | 1.049329 | 0.971605 | 0.012450 | 31.247426 |
19 rows × 24 columns
fig_spine = Plot(dataset, plot_name = 'new-fig-2')
fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'
fig_spine.display('jupyter-book', tissue = 'WM')